ParameterList-class          package:CALIB          R Documentation

_C_l_a_s_s "_P_a_r_a_m_e_t_e_r_L_i_s_t" - _L_i_s_t _t_o _s_t_o_r_e _a_l_l _t_h_e _p_a_r_a_m_e_t_e_r_s

_D_e_s_c_r_i_p_t_i_o_n:

     A simple list-based class for storing all the model parameters of
     a  batch of microarray.

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects can be created by calls of the form 'new("ParameterList",
     parameter)'  where parameter is a list. In the CALIB package,
     ParameterList objects are  normally generated by function
     'estimateParameter'.

_L_i_s_t _C_o_m_p_o_n_e_n_t_s:

     Objects should contain the following list components:

     '_M_u_S': Spot parameter. Mean of spot capacity.

     '_K_a': Hybridization constant.

     '_P_1': Respective slope of the linear dye saturation function. It
          is different for different dyes.

     '_P_2': Respective intercept of the linear dye saturation function.
          It is different for different dyes

     '_S_i_g_m_a_A': Standard deviation of additive error. It is different
          for different dyes.

     '_S_i_g_m_a_M': Standard deviation of multiplicative error.

     '_S_i_g_m_a_S': Spot parameter. Standard deviation of spot capacity.

     '_S_p_o_t_E_r_r_o_r': numeric matrix containing spot error of all external
          control spikes on arrays

     '_M_e_t_h_o_d': boolean values indicating the way to calculate the
          measured  intensities. It contains two subfields which are
          both logical value: BC and  Area. BC indicates whether
          background corrected measured intensities are used. Area
          indicates whether spot area is used to calculate measured
          intensities. 

     '_E_r_r_o_r_M_o_d_e_l': a character to represent the distribution of spot
          capacity. "L" means spot capacity follows 'log normal'
          distribution. "N" means spot  capacity follows 'normal'
          distribution.

     '_g_e_n_e_s': data.frame containing information on spikes spotted on
          the arrays. Should include a character column Name containing
          names for all the spikes.

     See reference for more detailed explaination for these list
     components.

_E_x_t_e_n_d_s:

     Class '"list"', from data part. Class '"vector"', by class
     '"list"'.

_M_e_t_h_o_d_s:

     This class inherits directly from class List. However since it
     represents the parameters  of the calibration model for arrays, it
     makes on sense to run functions like 'dim',  'dimnames',or 'merge'
     on this class.  Therefore, only some operations appropriate for
     list will work on objects of this class.  ParameterList objects
     can be 'cbind' and 'show' in a compact way.

     ParameterList objects are used on functions such as
     'normalizeData' or on some other data visualization functions like
     'plotSpikeHI' in the CALIB package.

_A_u_t_h_o_r(_s):

     Hui Zhao

_R_e_f_e_r_e_n_c_e_s:

     Engelen, K., Naudts, B., DeMoor, B., Marchal, K. (2006)  A
     calibration method for estimating absolute expression levels from 
     microarray data. Bioinformatics  22: 1251-1258.

